Any hopes that six imperiled Delta fish species might be trending back from the brink of extinction have been dashed by a new population survey: Counts for all six species got worse in 2012.

The species, all residents of the Sacramento-San Joaquin Delta, include Delta smelt, a protected finger-size fish, and striped bass, an introduced species that is a popular sportfish. All six saw a severe population crash starting in 2002 that is still the subject of debate and controversy.

The decline halted in 2011, when a wet winter improved aquatic habitat. All six species rebounded, though not to pre-2002 levels.

In the latest trawl-net survey of the estuary, conducted each fall since 1967, the gains of 2011 were lost. All six species returned to their prior low numbers, according to the survey, conducted by the California Department of Fish and Wildlife.

"In a nutshell, we just went back to the baseline. And it's not particularly good," said Randy Baxter, a supervising environmental scientist at the department.

One species, threadfin shad, set a record low population in the latest survey. The fish is not native to the Delta, but because it shares the same habitat, it is considered an important indicator of estuary health.

"The fact that it's doing poorly is indicative of a pretty broad-ranging problem," Baxter said.

Wildlife officials began their annual fall count of the six species decades ago because they are relatively easy to count by dragging a net through the water. The trend in their abundance is considered an important measure of the Delta's ecological productivity.

State and federal wildlife experts have spent a decade trying to understand why the species remain in steep decline. They have found no simple answer, but rather a combination of factors, including water diversions, pollution and competition with invasive species.

Baxter noted that 2012 was a relatively dry year, which may have contributed to the latest decline. Less rain and snowmelt runoff mean less aquatic habitat, less water to dilute pollutants, and changes in the way food is produced and available to fish.

The big controversy still clusters around freshwater flows into, and out of, the estuary. These flows are tightly controlled by California's vast network of dams, canals and pumps and the demands of the people and crops that depend on that infrastructure.

"What we're finding is that when flows are below a certain threshold, the (fish) populations are just going to continue to decline," said Jon Rosenfield, a conservation biologist at The Bay Institute, a nonprofit that supports revamping flows to benefit fish. "Last year, flows returned to their more recently normal state of being really bad, and all of the populations declined."

Because California has fully tapped the state's available water resources – parceling the flows among homes, farms, industry and wildlife – any adjustment to benefit fish necessarily comes at a cost to urban or agricultural water consumers.

Many water agencies that divert from the Delta point the finger for the species' declines at other culprits, such as water pollution, habitat losses and invasive species that eat native fish or displace their food.

Mike Wade, executive director of the California Farm Water Coalition, argues that instead of doing more about these other problems, regulators always move to curtail water exports when fish are imperiled.

"I think it's clear the effort to try and solve the problem by limiting exports is failing," Wade said. "That's the only knob we've been turning, so maybe that's not the solution."

Wildlife agencies turn that knob using the legal muscle of the Endangered Species Act. When a protected species such as Delta smelt shows up dead in water diversion systems, the diverters are required to take less water. The two major diversion pumping systems near Tracy are operated by the state Department of Water Resources and the U.S. Bureau of Reclamation.

No such pumping reductions were ordered to protect the six species during the 2012 water year, which ended Sept. 30, said Mike Chotkowski, Sacramento field supervisor for the U.S. Fish and Wildlife Service. The species likely benefitted, however, from pumping reductions carried out to protect salmon, which are not part of the latest survey.

Terry Erlewine, general manager of the State Water Contractors, said the salmon rules cost water diverters about 660,000 acre-feet in lost water supplies, or enough to serve more than 1.2 million households for a year.

Even so, the fish populations declined.

More recently, the Fish and Wildlife Service on Dec. 17 ordered pumping reductions to protect Delta smelt, after 90 were killed, or "entrained," at the pumps. The order was carried out partly because biologists have realized that smelt tend to favor muddy water. The fish seem to have an easier time finding food in muddy water, and it helps them hide from predators.

In flood conditions on the Sacramento River, this muddy or "turbid" water is drawn toward the pumps, and so are the smelt.

Chotkowski said the latest pumping reductions helped protect smelt. The numbers of fish killed dropped off sharply once the pumps began drawing less turbidity through the Delta.

"I think we'd be quite a bit worse off if we had not taken this action," he said.

Erlewine estimates the latest pumping cutbacks cost about 300,000 acre-feet in lost water deliveries. But he agreed it may have been beneficial to the smelt. If short-term cutbacks keyed to turbidity prove effective, he said, it may prevent more painful cuts.

"We've been interested in figuring out ways ... to avoid having the high pumping when turbidity is there," Erlewine said. "There's been a fairly high water cost. I think we're all learning in this."

ENVIRONMENTLEARN MORE: The Delta fish population data can be found online at http://ht.ly/gCbBn

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